Embedded-Hacking/WEEK04/WEEK04-BN.md

Week 4-BN: Binary Ninja Personal — Resolve, Hack, and Patch the RP2350 (Raw .bin)

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LEGAL DISCLAIMER: The information, tools, and code provided in this repository and course are strictly for educational, research, and defensive purposes only.

You are explicitly prohibited from using any materials contained herein to access, test, modify, or exploit any device, network, or system that you do not own 100% or for which you do not have explicit, documented, and legally binding authorization to interact with.

By using this repository and course, you acknowledge and agree that:

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IF YOU DO NOT AGREE WITH THESE TERMS, DO NOT USE THIS REPOSITORY AND COURSE.

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What You'll Learn This Week

• Build the two lesson projects with Release and get both an .elf and a raw .bin
• Dump the ELF symbol map with arm-none-eabi-nm and use it as ground truth
• Load the raw .bin into Binary Ninja at 0x10000000
• Break at main on live silicon, even though main can move between programs
• Hack a running target live by editing a register in Binary Ninja's Registers widget
• Resolve the functions in the Binary Ninja GUI using the ELF symbol map
• Patch the bytes that control the behavior, export the image, and flash it

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How This Guide Works

The build produces two files for each project:

File	What it is	How we use it
.elf	The linked image with a full symbol table	Ground truth for every function address and name
.bin	The raw flash image, no headers, no symbols	The image we load into Binary Ninja and reverse

The .bin is built from the .elf, so the ELF tells you exactly what is at every address. We use the ELF symbol map to resolve functions in Binary Ninja, and we reverse-engineer the raw .bin the way a real extracted firmware image is reversed.

Build Release, not Debug. Every address in this guide matches the Week 4 lesson, and the Week 4 lesson is a Release build. Release optimizes the code the same way the original lesson was built: it folds age = 42 away in Project 1 and inlines blink_and_print into main in Project 2. If you build Debug, the SDK function addresses move and Project 2 keeps a separate blink_and_print, so nothing lines up. Always build Release for this lesson.

The order is dynamic first, static second, twice — once per project:

1. Break on the live target and prove what the code does.
2. Hack it live in the debugger and watch the behavior change.
3. Resolve the functions in Binary Ninja using the ELF symbol map.
4. Patch the bytes, export, convert, and flash.

Project	Prints	Also does	The hack
0x0005_intro-to-variables	age: 43	loops on printf	change 43 to 70
0x0008_uninitialized-variables	age: 0	blinks the red LED on GPIO 16	change 0 to 66, move the LED to GPIO 17

Addresses come from your build. Every address here is from the Release build produced in Step 3. Confirm against your own .elf with the command in Step 4.

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Part 1: Build, Flash, and Get the Symbol Map

Step 1: Install the toolchain

Windows x64

• Install the Raspberry Pi Pico extension in VS Code. It installs the ARM GNU toolchain, CMake, Ninja, and the Pico SDK.
• Install Binary Ninja Personal and complete its license activation.
• Install PuTTY for the serial monitor.

macOS Apple Silicon

brew install cmake ninja

• Install Binary Ninja Personal and complete its license activation.
• Install the Arm GNU Toolchain, or let the VS Code Pico extension manage it.

Linux x64

sudo apt install cmake ninja-build gcc-arm-none-eabi libnewlib-arm-none-eabi git python3 openocd minicom

• Install Binary Ninja Personal and complete its license activation.

Step 2: Verify your tools are the right architecture (do not skip this)

On macOS Apple Silicon, the most common failure is an Intel x86_64 tool on your PATH:

zsh: bad CPU type in executable: cmake

You may have two Homebrews: the arm64 one at /opt/homebrew and the Intel one at /usr/local. If /usr/local/bin wins, every brew tool is x86_64. Check:

file "$(which cmake)"
file "$(which ninja)"
file "$(which arm-none-eabi-gdb)"
file "$(which arm-none-eabi-nm)"
file "$(which openocd)"
file "$(which telnet)"

All must report arm64. If any is x86_64, put the Apple Silicon prefix first for the session and check again:

export PATH="/opt/homebrew/bin:$PATH"
hash -r
file "$(which cmake)"

To make it permanent, add that export to ~/.zshrc. Do not use Rosetta as a fix; OpenOCD and GDB are exactly the kind of programs where a translation layer produces failures that look like debugger bugs.

telnet is special — and optional. The GDB MI workflow does not need it; it is only used by the command-port fallback. macOS no longer ships telnet, and the Homebrew build is often the Intel one, so telnet 127.0.0.1 4444 fails with bad CPU type in executable. Your brew command itself may also be the Intel one: if brew install telnet fails with .../portable-ruby/.../ruby: Bad CPU type in executable, you are running the Intel Homebrew. Call the Apple Silicon Homebrew explicitly:

/opt/homebrew/bin/brew install telnet

If you would rather not install anything, macOS ships an arm64 nc, which can connect to the same OpenOCD port:

nc 127.0.0.1 4444

Windows x64 and Linux x64 do not have this problem. Skip to Step 3.

Step 3: Build the two projects with Release

Run this once inside 0x0005_intro-to-variables/ and once inside 0x0008_uninitialized-variables/:

cmake -B build -G Ninja -DPICO_BOARD=pico2 -DPICO_PLATFORM=rp2350 -DCMAKE_BUILD_TYPE=Release
cmake --build build

Point Binary Ninja at this repository (once). Every console snippet below reads the repo root from ~/.embedded-hacking-repo, so Binary Ninja never needs a database open and nothing is hardcoded. From the repo root, run once:

macOS / Linux:

pwd > ~/.embedded-hacking-repo

Windows (PowerShell):

(Get-Location).Path | Set-Content "$env:USERPROFILE\.embedded-hacking-repo"

Then build from the Binary Ninja console, so the whole build -> patch -> flash loop stays inside Binary Ninja. The console inherits a minimal PATH — on macOS just /usr/bin:/bin:/usr/sbin:/sbin — so it does not see Homebrew; add your package manager's bin first, then run plain cmake.

macOS Apple Silicon:

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()
os.environ["PATH"] = "/opt/homebrew/bin:" + os.environ["PATH"]  # the console's PATH omits Homebrew
for name in ("0x0005_intro-to-variables", "0x0008_uninitialized-variables"):
    proj = os.path.join(root, name)
    subprocess.run(["cmake", "-B", "build", "-G", "Ninja", "-DPICO_BOARD=pico2",
                    "-DPICO_PLATFORM=rp2350", "-DCMAKE_BUILD_TYPE=Release"], cwd=proj)
    subprocess.run(["cmake", "--build", "build"], cwd=proj)

Linux x64:

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()
for name in ("0x0005_intro-to-variables", "0x0008_uninitialized-variables"):
    proj = os.path.join(root, name)
    subprocess.run(["cmake", "-B", "build", "-G", "Ninja", "-DPICO_BOARD=pico2",
                    "-DPICO_PLATFORM=rp2350", "-DCMAKE_BUILD_TYPE=Release"], cwd=proj)
    subprocess.run(["cmake", "--build", "build"], cwd=proj)

Windows x64:

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()
for name in ("0x0005_intro-to-variables", "0x0008_uninitialized-variables"):
    proj = os.path.join(root, name)
    subprocess.run(["cmake", "-B", "build", "-G", "Ninja", "-DPICO_BOARD=pico2",
                    "-DPICO_PLATFORM=rp2350", "-DCMAKE_BUILD_TYPE=Release"], cwd=proj)
    subprocess.run(["cmake", "--build", "build"], cwd=proj)

Each build directory now contains the pair we need:

• 0x0005_intro-to-variables/build/0x0005_intro-to-variables.elf and .bin — .bin is 15292 bytes
• 0x0008_uninitialized-variables/build/0x0008_uninitialized-variables.elf and .bin — .bin is 15668 bytes

If the ARM toolchain is not on your PATH, add -DPICO_TOOLCHAIN_PATH=...:

OS	Typical toolchain path
Windows x64	C:/Program Files/Arm GNU Toolchain arm-none-eabi/14.2 rel1/bin
macOS Apple Silicon	/Applications/ArmGNUToolchain/14.2.rel1/arm-none-eabi/bin
Linux x64	/usr

Step 4: Dump the ELF symbol map

This is the ground truth for the whole lesson. Run arm-none-eabi-nm on each ELF and keep the output in a terminal or a text file:

macOS Apple Silicon / Linux x64:

arm-none-eabi-nm -n --defined-only build/0x0005_intro-to-variables.elf | grep -E ' [Tt] '
arm-none-eabi-nm -n --defined-only build/0x0008_uninitialized-variables.elf | grep -E ' [Tt] '

Windows x64:

arm-none-eabi-nm -n --defined-only build\0x0005_intro-to-variables.elf | Select-String ' [Tt] '

Each line is address type name. The T/t type is a function. Here are the functions this lesson uses.

Project 1 — 0x0005_intro-to-variables:

Address	ELF symbol	Signature	Role
0x1000015c	_reset_handler	void _reset_handler(void)	reset entry
0x10000186	platform_entry	void platform_entry(void)	calls runtime_init, main, exit
0x1000019a	data_cpy	void data_cpy(void*, void*, void*)	copies .data from flash to SRAM
0x100001e4	_init	void _init(void)	runs .init_array
0x10000210	frame_dummy	void frame_dummy(void)	C runtime boilerplate
0x10000234	main	int main(void)	the lesson function
0x10000248	gpio_set_function	void gpio_set_function(uint, gpio_function_t)	SDK GPIO helper
0x10002cfc	exit	void exit(int)	C runtime exit
0x10002d04	runtime_init	void runtime_init(void)	SDK runtime init
0x10002f54	stdio_init_all	bool stdio_init_all(void)	SDK serial init
0x100030e4	__wrap_printf	int __wrap_printf(const char*, ...)	the printf wrapper

These signatures come from the ELF's DWARF debug info, so they are exact. You apply them in Binary Ninja in Step 16 (G -> address, then Y -> Change Type).

Project 2 — 0x0008_uninitialized-variables:

Address	ELF symbol	Signature	Role
0x1000015c	_reset_handler	void _reset_handler(void)	reset entry
0x10000186	platform_entry	void platform_entry(void)	calls runtime_init, main, exit
0x1000019a	data_cpy	void data_cpy(void*, void*, void*)	copies .data from flash to SRAM
0x100001e4	_init	void _init(void)	runs .init_array
0x10000210	frame_dummy	void frame_dummy(void)	C runtime boilerplate
0x10000234	main	int main(void)	the lesson function (blink_and_print inlined)
0x10000278	gpio_set_function	void gpio_set_function(uint, gpio_function_t)	SDK GPIO helper
0x100002b4	gpio_init	void gpio_init(uint)	SDK GPIO init
0x10000d10	sleep_ms	void sleep_ms(uint32_t)	SDK delay
0x10002e74	exit	void exit(int)	C runtime exit
0x10002e7c	runtime_init	void runtime_init(void)	SDK runtime init
0x100030cc	stdio_init_all	bool stdio_init_all(void)	SDK serial init
0x1000325c	__wrap_printf	int __wrap_printf(const char*, ...)	the printf wrapper

main is 0x10000234 in both projects. In Project 2 the static void blink_and_print helper is inlined into main by the Release optimizer, so it does not appear as a separate symbol. That is why both projects put main at the same address. In a Debug build it stays separate and main moves — another reason to build Release.

Step 5: Flash Project 1 and confirm age: 43

A .bin has no headers, so OpenOCD must be told the base address 0x10000000. From the repository root:

macOS Apple Silicon / Linux x64:

./flash.sh 0x0005_intro-to-variables/build/0x0005_intro-to-variables.bin

Windows x64 (PowerShell):

.\flash.ps1 -Bin 0x0005_intro-to-variables\build\0x0005_intro-to-variables.bin

Or flash from the Binary Ninja console (with a database open, so the repo root is taken from it — otherwise use the terminal form above):

macOS Apple Silicon / Linux x64:

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()  # set once (Step 3)
bin_path = os.path.join(root, "0x0005_intro-to-variables", "build", "0x0005_intro-to-variables.bin")
log = os.path.join(os.path.dirname(bin_path), "flash.log")
subprocess.run(["pkill", "-TERM", "-f", "openocd"])  # free the probe first
subprocess.Popen([os.path.join(root, "flash.sh"), bin_path],
                 stdout=open(log, "w"), stderr=subprocess.STDOUT, start_new_session=True)
print("flashing in the background; log:", log)

Windows x64:

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()  # set once (Step 3)
bin_path = os.path.join(root, "0x0005_intro-to-variables", "build", "0x0005_intro-to-variables.bin")
log = os.path.join(os.path.dirname(bin_path), "flash.log")
subprocess.run(["taskkill", "/F", "/IM", "openocd.exe"])  # free the probe first
subprocess.Popen(["powershell", "-ExecutionPolicy", "Bypass", "-File",
                  os.path.join(root, "flash.ps1"), "-Bin", bin_path],
                 stdout=open(log, "w"), stderr=subprocess.STDOUT)
print("flashing in the background; log:", log)

Wait for wrote 15292 bytes ... and ** Verified OK **. Open a serial monitor at 115200 baud:

• Windows x64: PuTTY -> Connection type Serial, the Pico's COM port, speed 115200.
• macOS Apple Silicon: screen /dev/tty.usbmodem* 115200 (quit with Ctrl-A then K).
• Linux x64: minicom -D /dev/ttyACM0 -b 115200.

age: 43
age: 43
age: 43
...

Step 6: Flash Project 2 and confirm age: 0 + red LED

# macOS / Linux
./flash.sh 0x0008_uninitialized-variables/build/0x0008_uninitialized-variables.bin

# Windows
.\flash.ps1 -Bin 0x0008_uninitialized-variables\build\0x0008_uninitialized-variables.bin

Or flash from the Binary Ninja console (same form as Step 5, pointing at the Project 2 .bin):

macOS / Linux:

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()  # set once (Step 3)
bin_path = os.path.join(root, "0x0008_uninitialized-variables", "build", "0x0008_uninitialized-variables.bin")
log = os.path.join(os.path.dirname(bin_path), "flash.log")
subprocess.run(["pkill", "-TERM", "-f", "openocd"])
subprocess.Popen([os.path.join(root, "flash.sh"), bin_path],
                 stdout=open(log, "w"), stderr=subprocess.STDOUT, start_new_session=True)
print("flashing in the background; log:", log)

Windows:

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()  # set once (Step 3)
bin_path = os.path.join(root, "0x0008_uninitialized-variables", "build", "0x0008_uninitialized-variables.bin")
log = os.path.join(os.path.dirname(bin_path), "flash.log")
subprocess.run(["taskkill", "/F", "/IM", "openocd.exe"])
subprocess.Popen(["powershell", "-ExecutionPolicy", "Bypass", "-File",
                  os.path.join(root, "flash.ps1"), "-Bin", bin_path],
                 stdout=open(log, "w"), stderr=subprocess.STDOUT)
print("flashing in the background; log:", log)

Wait for wrote 15668 bytes .... The serial monitor shows:

age: 0
age: 0
age: 0
...

and the red LED on GPIO 16 blinks once per second.

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Part 2: Load the Raw .bin into Binary Ninja

Start from a fresh Binary Ninja state. If you already have a .bndb for this lesson, close it and start over; a stale database keeps old names and patches.

Step 7: Bring the raw .bin into Binary Ninja

A raw .bin has no headers, so Binary Ninja cannot know where it belongs or what architecture it is. You must supply both. If you just double-click the .bin, Binary Ninja may load it at address 0x0 with a guessed architecture, and every address in this lesson will be wrong.

1. Choose File -> Open with Options... (do not use plain File -> Open).
2. Select 0x0005_intro-to-variables/build/0x0005_intro-to-variables.bin.
3. In the loader options, set:
   • Architecture: thumb2 (the ARMv7-M / ARMv8-M Thumb-2 architecture, which covers the Cortex-M33)
   • Platform: thumb2
   • Base Address: 0x10000000 (the XIP flash base)
4. Click Open.

Binary Ninja analyzes the image and opens the linear view.

Verify the load before going further. Press G, type 0x10000000, and read the first two words:

0x10000000   0x20082000   initial stack pointer
0x10000004   0x1000015d   reset vector (bit 0 = Thumb)

If you instead see data at 0x00000000, or a vector word without bit 0 set, close the tab and repeat with Open with Options. The Cortex-M33 only executes Thumb-2, so thumb2 is the only correct architecture.

Console equivalent:

load("0x0005_intro-to-variables/build/0x0005_intro-to-variables.bin",
     options={"loader.imageBase": 0x10000000, "loader.platform": "thumb2"})

Step 8: Save it as a Binary Ninja database (.bndb)

Binary Ninja never writes back into the .bin. Your names, comments, types, and patches live in a separate .bndb database. Save one now, before you make any changes:

1. Choose File -> Save As....
2. Save it next to the image as 0x0005_intro-to-variables.bndb.
3. From now on, save with File -> Save (Cmd+S on macOS, Ctrl+S on Windows/Linux) whenever you rename or patch.

The two files have different roles:

File	Role
0x0005_intro-to-variables.bin	the raw firmware image; Binary Ninja never modifies it
0x0005_intro-to-variables.bndb	your analysis database: names, types, comments, and patches

When you come back later, open the .bndb, not the .bin; that restores all your work. If a database gets messy, delete the .bndb and re-import the .bin from Step 7 — the firmware is never at risk. You export the patched image out of this view later, in Step 19.

Step 9: The views you will use

• Linear view: the disassembly listing. You navigate, read, and patch here.
• Graph view: the control-flow graph of the current function.
• Decompiler (HLIL): the pseudo-C decompilation.
• Hex view: raw bytes, used for patching.
• Function list: the sidebar list of every detected function.

Navigation: G go to address, N rename, Y set type or signature, ; add a comment. Breakpoints are set from the OpenOCD command port, not from the GUI — see Step 13.

macOS function keys: the top-row F keys are usually mapped to system functions. Every step here uses menu paths that work without them.

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Part 3: Dynamic — Break at main and Hack Live (Project 1)

Step 10: Start OpenOCD as a live debug server

Make sure no other OpenOCD is running; a forgotten server holds port 3333.

macOS / Linux:

ps aux | grep -i openocd

Windows (PowerShell):

Get-Process | Where-Object { $_.ProcessName -like '*openocd*' }

Stop any leftover server gracefully:

macOS / Linux:

pkill -TERM -f openocd

Windows (PowerShell):

Get-Process openocd -ErrorAction SilentlyContinue | Stop-Process

Start the server parked at main:

macOS Apple Silicon / Linux x64:

BP_ADDR=0x10000234 ./debug-server.sh

Windows x64 (PowerShell):

$env:BP_ADDR="0x10000234"; .\debug-server.ps1

Or start it from the Binary Ninja console, freeing the probe first and launching the server in the background so the console returns immediately:

macOS Apple Silicon / Linux x64:

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()  # set once (Step 3)
subprocess.run(["pkill", "-TERM", "-f", "openocd"])  # stop any running server first
log = os.path.join(root, "openocd.log")
p = subprocess.Popen([os.path.join(root, "debug-server.sh")], cwd=root,
                     env=dict(os.environ, BP_ADDR="0x10000234"),
                     stdout=open(log, "w"), stderr=subprocess.STDOUT, start_new_session=True)
print("OpenOCD started (pid", p.pid, "); log:", log)

Windows x64:

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()  # set once (Step 3)
subprocess.run(["taskkill", "/F", "/IM", "openocd.exe"])  # stop any running server first
log = os.path.join(root, "openocd.log")
p = subprocess.Popen(["powershell", "-ExecutionPolicy", "Bypass", "-File",
                      os.path.join(root, "debug-server.ps1")], cwd=root,
                     env=dict(os.environ, BP_ADDR="0x10000234"),
                     stdout=open(log, "w"), stderr=subprocess.STDOUT)
print("OpenOCD started (pid", p.pid, "); log:", log)

Popen returns in a few milliseconds; the server keeps running in the background. Check openocd.log for Listening on port 3333, then connect in Step 11.

Wait for:

Info : [rp2350.dap.core0] Examination succeed
Startup breakpoint at 0x10000234 (2-byte hardware execute, one-shot).
Info : starting gdb server for rp2350.dap.core0 on 3333
Info : Listening on port 3333 for gdb connections

BP_ADDR parks the core at main before any client connects. The script arms a 2-byte hardware breakpoint and then does the startup reset run, so the core runs from the vector table and stops at your address with no debugger attached yet. When Binary Ninja connects a moment later, the first thing it reads is already the truth: Stopped at 0x10000234. This is the whole reason the lab works cleanly — you never have to drive a reset from outside the GUI.

Use the address you actually want to stop at:

What you want to stop at	Project 1 0x0005	Project 2 0x0008	Command
main (once per reset)	0x10000234	0x10000234	BP_ADDR=0x10000234 ./debug-server.sh
The loop — the printf call, hit every iteration	0x1000023e	0x1000024e	BP_ADDR=0x1000023e ./debug-server.sh

BP_ADDR=0x10000234 ./debug-server.sh   # park at main
BP_ADDR=0x1000023e ./debug-server.sh   # park in the loop instead

$env:BP_ADDR="0x10000234"; .\debug-server.ps1   # park at main
$env:BP_ADDR="0x1000023e"; .\debug-server.ps1   # park in the loop

Note the loop address is not the same in both projects. Project 2 does more setup before the loop, so its bl __wrap_printf sits at 0x1000024e, not 0x1000023e. Both were verified against the Release .elf with arm-none-eabi-objdump and confirmed live on hardware.

This startup stop is single-use. OpenOCD flushes breakpoints when a client connects, so this one is gone once Binary Ninja attaches — fine for main, which only runs once per reset. Every breakpoint after that is set from the Binary Ninja GUI (Step 13) and is repeatable. To stop at main again, restart the server with BP_ADDR and reconnect.

Exactly one core. The line must say core0 and must not mention core1. Core1 is never started by this firmware; exposing it makes Binary Ninja read core1's reset-state registers, which are not real addresses, and OpenOCD floods the log with Failed to read memory at 0xf0000000. The scripts already use USE_CORE=0; do not change it.

Windows driver note: the Debug Probe must use the WinUSB driver. If OpenOCD reports unable to open CMSIS-DAP device, install it with Zadig (select Debug Probe (CMSIS-DAP) -> WinUSB).

Step 11: Connect Binary Ninja to the GDB server

1. Make sure the image is open and analyzed (Part 2) and the server from Step 10 is running (parked at main).
2. Choose Debugger -> Connect to Remote Process.
3. In the adapter dropdown, select GDB MI.
4. In the connect settings group, set IP Address to 127.0.0.1 and Port to 3333.
5. Set Full GDB Executable Path to your arm-none-eabi-gdb. On macOS the build that works is the 14.2.rel1 toolchain:

   /Applications/ArmGNUToolchain/14.2.rel1/arm-none-eabi/bin/arm-none-eabi-gdb
   

6. Click Accept.

Use the GDB MI adapter. It launches a real arm-none-eabi-gdb --interpreter=mi2 and lets Binary Ninja drive it, so breakpoints and stepping go through real GDB — which sends the correct 2-byte breakpoint length and handles step-over itself. Verified working end to end: connect, GUI breakpoints (Add Hardware Breakpoint..., hardware execute), Step Into / Step Over, and register edits. Stops are reported as Breakpoint (not SingleStep).

Do NOT have any breakpoints set in Binary Ninja before you connect. With the GDB MI adapter, attaching while Binary Ninja already has a breakpoint hangs the session. Start the server parked with BP_ADDR (Step 10), connect, and only add hardware breakpoints after the connection is up. This is a Binary Ninja bug; it is the single most common GDB MI failure.

The GDB executable path matters. Use the 14.2.rel1 build above. The 13.3.rel1 build — which is what /opt/homebrew/bin/arm-none-eabi-gdb symlinks to — did not connect in testing.

Do not pick Corellium. Binary Ninja's adapter dropdown also lists Corellium, which is for Corellium's virtual devices and expects an API token, not a local OpenOCD server. It is not the adapter for this lab. The dropdown is a combo box, so an accidental arrow-key press can land on it — always read the label back and confirm it says GDB MI before clicking Accept.

The adapter and port are not saved in the .bndb. Every time you relaunch Binary Ninja you must re-select GDB MI, re-enter port 3333, and re-set the GDB path.

Watch for an off-screen error dialog. When a connection fails, Binary Ninja pops a Binary Ninja critical alert window that can be positioned mostly outside the main window (seen at 2430,331 with the main window at 2560,30), which makes it look like nothing happened. If the connect seems to do nothing, check your other display.

The target keeps running. Open the Registers tab (bug icon) and confirm you see live values. pc inside 0x10003xxx and sp just below 0x20082000 are healthy.

If pc is 0x00000088, 0x000000ec, or sp is 0xf0000000, the session is bad. Restart the server, then restart Binary Ninja (a server restart while attached leaves Binary Ninja in a stale session), and connect again.

Step 12: Find main without relying on its address

main can move between programs, so we do not guess it. We follow the one fixed path to it. Press G and go to 0x10000000:

0x10000000   0x20082000   initial stack pointer (top of SRAM)
0x10000004   0x1000015d   reset vector

Bit 0 of a vector is the Thumb bit, so 0x1000015d means "start at 0x1000015c". That is _reset_handler. Follow the reset path to 0x10000186, platform_entry:

10000186 <platform_entry>:
10000186: 4914   ldr  r1, [pc, #80] ; @ 0x100001d8
10000188: 4788   blx  r1            ; runtime_init
1000018a: 4914   ldr  r1, [pc, #80] ; @ 0x100001dc
1000018c: 4788   blx  r1            ; main  <-- the fixed anchor
1000018e: 4914   ldr  r1, [pc, #80] ; @ 0x100001e0
10000190: 4788   blx  r1            ; exit
10000192: be00   bkpt 0x0000

The middle blx at 0x1000018c is the call to main. platform_entry is byte-identical in both projects, so 0x1000018c catches main no matter where the linker placed it. The literal pool at 0x100001dc holds main | 1, and clearing bit 0 gives 0x10000234.

Step 13: Set a hardware breakpoint in the GUI

With the GDB MI adapter, Binary Ninja sets breakpoints through real GDB, which sends the correct 2-byte length, so you set them in the UI. There is no command port here.

Why older drafts used the command port. Binary Ninja's GDB RSP adapter is its own minimal RSP client and sends a 1-byte breakpoint (Z0,<addr>,1); the Cortex-M33 FPB comparators need 2 bytes, so OpenOCD rejected it with only breakpoints of two bytes length supported. The old workaround was to arm breakpoints by hand over telnet. The GDB MI adapter does not have this problem — it drives real arm-none-eabi-gdb, which sends the right length. So everything below is done in the GUI. The command port still exists as a fallback (see the end of this step), but you do not need it.

Where you can stop

You want to stop at	Address	How	Repeatable?
main	0x10000234	The server starts parked there with BP_ADDR=0x10000234 (Step 10), so Binary Ninja is already stopped at main when it connects.	No — main runs once per reset.
The loop (printf call)	Project 1 0x1000023e, Project 2 0x1000024e	Set a hardware breakpoint in the GUI, then click Resume.	Yes — fires on every iteration.

Set the loop breakpoint in the GUI

1. Press G, type the loop address (0x1000023e for Project 1, 0x1000024e for Project 2), and press Enter.
2. Set a hardware execution breakpoint at that address, either way:
   • Debugger -> Add Hardware Breakpoint... — a hardware execute (HE) breakpoint. Use this one.
   • click the line and press F2 (Debugger -> Toggle Breakpoint) — a software breakpoint. It will not work here: the code is in read-only flash, so GDB cannot install it and the core just keeps running.
3. Click Resume. The core is already running the loop, so the breakpoint fires on the next iteration. Binary Ninja stops with the PC at the loop address and reports it as a Breakpoint — verified: Stopped (Breakpoint) at 0x1000023e.

No breakpoints before you connect. With GDB MI, a breakpoint set before the connection hangs the session (Step 11). Start parked with BP_ADDR, connect, then add breakpoints.

Stepping

With the target halted at the breakpoint, Step Into (F7) and Step Over (F8) run through real GDB and move the PC. Verified: 0x1000023e -> 0x100030e4 -> 0x100030e6 -> ....

Step Over on the raw .bin steps into calls. The raw image has no symbol for __wrap_printf, so Step Over at the printf call behaves like Step Into. When the lab needs to execute the call and then stop, it moves the breakpoint to the return site and clicks Resume instead (Step 14 shows this).

Never use Binary Ninja's Restart button. On RP2350 it resets and halts inside the boot ROM (pc=0x88, sp=0xf0000000). To reset cleanly, restart the server with BP_ADDR and reconnect.

If you ever need the command port. It is still there — nc 127.0.0.1 4444, and bp <addr> 2 hw still arms a breakpoint, rbp <addr> / rbp all still remove them. It is the fallback if you switch back to the GDB RSP adapter, whose 1-byte breakpoints the GUI cannot set. With GDB MI you do not need it for this lab.

Step 14: HACK IT LIVE — change the printed value

main loads the constant 0x2b (43) into r1 and calls printf on every iteration. We break on that call in the GUI and change it live.

1. Press G, go to 0x1000023e (the bl __wrap_printf).

2. Set a hardware execute breakpoint there: Debugger -> Add Hardware Breakpoint.... (Do not use F2 — that is a software breakpoint and will not work on read-only flash.)

3. Click Resume in Binary Ninja. The target is already running the loop, so the breakpoint fires on the next iteration. Binary Ninja stops with the program counter at 0x1000023e and r1 = 0x2b.

4. Open the Registers widget (bug icon -> Registers).

5. Find r1. Its value is 0x2b.

6. Set r1 to 0x46. From Binary Ninja's Python console (Plugins -> Python Console):

   dbg.set_reg_value("r1", 0x46)
   

   dbg.set_reg_value(name, value) writes one register (returns True on success). You can also right-click r1 in the Registers widget, press E (edit), type 46, and press Enter. The widget may not repaint the value, but the write reaches the target — you confirm it by the printed output in the next steps.

7. Move the breakpoint past the call. You want printf to run once and then stop, so move the breakpoint from 0x1000023e to the instruction after the call, 0x10000242 (the b.n that closes the loop): remove the breakpoint at 0x1000023e and set a hardware breakpoint at 0x10000242. Two reasons not to just click Step Over here: a breakpoint left on the current PC re-traps the step, and Binary Ninja's Step Over steps into __wrap_printf on this raw .bin because the image carries no symbol for the call. Moving the breakpoint to the return site is deterministic.

8. Click Resume in Binary Ninja. The core executes bl __wrap_printf with r1 = 0x46, so this iteration prints age: 70, then stops at 0x10000242.

9. Look at your serial monitor — the screen session on the Pico's USB serial port — and at the Target tab in Binary Ninja:

   age: 70
   

You changed a running program's output without touching the binary.

Step 14b: HACK THE STRING LIVE — change age: to foo:

The text "age: %d\r\n" lives in flash (.rodata) at 0x100034a0, and flash is read-only at runtime — a debugger write there does not stick (verified: writing 0x66 to 0x100034a0 read back unchanged). So you cannot overwrite the text in place. Instead you redirect the pointer: at the printf call, r0 holds the string address, so you point r0 at a replacement string you place in RAM.

1. Arm the breakpoint at the printf call and hit it, exactly as in Step 14 steps 1-3. At the stop, r0 = 0x100034a0 and r1 = 0x2b.
2. Put the replacement string into free RAM at 0x20080000 from Binary Ninja's Python console (Plugins -> Python Console) — no command port needed:

   dbg.write_memory(0x20080000, b"foo: %d\r\n\x00")
   

   dbg.write_memory(address, bytes) is Binary Ninja's debugger memory-write API; it returns True on success. That writes the bytes 66 6f 6f 3a 20 25 64 0d 0a 00 = "foo: %d\r\n\0".
3. Point r0 at that string:

   dbg.set_reg_value("r0", 0x20080000)
   

   (Or right-click r0 in the Registers widget, press E, type 0x20080000, and press Enter.)
4. Move the breakpoint past the call in the GUI (remove it at 0x1000023e, set one at 0x10000242) and click Resume. The core runs printf with r0 pointing at your RAM string and r1 = 0x2b, so this iteration prints:

   foo: 43
   

   then stops at 0x10000242.

Like the value hack, this is one iteration only: the loop reloads r0 (and r1) from flash on every pass, so the next line is age: 43 again. The permanent version is the static patch in Step 19b.

Step 15: Why the hack reverts (and why we patch next)

Press Resume. The loop branches back to 0x1000023a, which reloads movs r1, #43, so the next line is age: 43. The live edit changed one iteration only. There is no variable in memory to change; the value is baked into the instruction. To make age: 70 permanent we must patch the instruction. That is the static pass.

Press Pause to stop the output flood.

Step 15b: Kill the debugger and OpenOCD

The live hack is done. Do this before the static pass.

1. In the Debugger sidebar, click the X (Kill) (or Debugger -> Kill) to disconnect Binary Ninja.

2. Kill does not stop the OpenOCD process — debug-server.sh started it separately, and it keeps running and holding the probe. Stop it from the Binary Ninja console:

   macOS / Linux:

   import subprocess
   subprocess.run(["pkill", "-TERM", "-f", "openocd"])  # stop the debug server, free the probe
   

   Windows:

   import subprocess
   subprocess.run(["taskkill", "/F", "/IM", "openocd.exe"])  # stop the debug server, free the probe
   

3. Confirm nothing is left: pgrep -fl openocd (macOS/Linux) prints nothing.

From a terminal it is the same: pkill -TERM -f openocd, or Get-Process openocd | Stop-Process on Windows.

---

Part 4: Static — Resolve the Functions in Binary Ninja and Patch (Project 1)

Step 16: Resolve the functions in the Binary Ninja GUI

We now name the functions in Binary Ninja using the ELF symbol map from Step 4. Binary Ninja loaded the raw .bin with no symbols, so every function shows as sub_<addr> — resolving means giving each one its real name and signature.

Three keys do all the work:

Key	Binary Ninja action	Use it for
G	Go to address	Jump to a function's address
Y	Change Type	Set the function's signature. The dialog shows the full prototype, so this sets the name and the type in one step.
N	Rename	Rename only, when you just want the name and not the type

For each function below: G to its address, then Y (Change Type) and type the prototype from the table.

How to resolve a function in Binary Ninja (Y)

Y is the Change Type key, and it is what actually resolves the function — it turns void sub_10002f54() into bool stdio_init_all(void). The Change Type dialog shows the full declaration (name and type), so typing the prototype sets both:

1. G to the function's address. The cursor lands on the function.
2. Press Y. In the Change Type dialog, type the prototype from the table exactly — for example bool stdio_init_all(void) — and press Enter.

The decompiler header then shows the real prototype, and calls to the function read cleanly instead of sub_<addr>(). N is only for renaming without touching the type; Y alone sets both the name and the type.

If Y seems to do nothing, confirm the cursor is on the function, or right-click it and pick Change Type.... Binary Ninja parses what you type and silently keeps the old type if it does not parse, so glance at the header after each Y.

Worked example: main

1. Press G, type 0x10000234, press Enter. The view jumps there; the cursor lands on sub_10000234.
2. Press Y (Change Type), type int main(void), press Enter. That sets the name to main and the type to int(void).

Binary Ninja shows int32_t where Ghidra shows int. After you set int main(void), the decompiler header may read int32_t main(void). That is the same type — on this platform int is 32 bits and Binary Ninja's parser normalises it to int32_t. Do not fight it; it is not an error.

Worked example: stdio_init_all

1. G -> 0x10002f54.
2. Y -> bool stdio_init_all(void).

It returns bool, not void — the ELF says _Bool stdio_init_all(void). Our main ignores the return value, so the decompiler still reads cleanly.

Worked example: uart_init

1. G -> 0x10000e10.
2. Y -> uint uart_init(uart_inst_t *uart, uint baudrate).

Worked example: __wrap_printf

1. G -> 0x100030e4.
2. Y -> int __wrap_printf(const char *fmt, ...). Keep the ... — printf is variadic.

printf in our source is __wrap_printf in the binary. The SDK links our printf calls to its __wrap_printf wrapper.

The rest of the chain is the same two keystrokes per function (G, then Y). This is our code plus the library functions it actually calls — not the whole SDK. main only calls stdio_init_all and printf, so we follow that chain down: stdio_init_all pulls in the stdio/UART setup, and printf lands in the SDK's __wrap_printf.

The call chain for this project:

main
├── stdio_init_all
│   ├── stdio_uart_init ── gpio_set_function, uart_init
│   ├── stdio_set_driver_enabled
│   ├── stdio_out_chars_crlf
│   ├── stdio_put_string ── strlen
│   └── time_us_64
└── __wrap_printf ── __wrap_vprintf

Project 1 — resolve every function in that chain:

Address	Rename to (N)	Signature (Y)
0x1000015c	_reset_handler	void _reset_handler(void)
0x10000186	platform_entry	void platform_entry(void)
0x1000019a	data_cpy	void data_cpy(void*, void*, void*)
0x100001e4	_init	void _init(void)
0x10000210	frame_dummy	void frame_dummy(void)
0x10000234	main	int main(void)
0x10002cfc	exit	void exit(int)
0x10002d04	runtime_init	void runtime_init(void)
0x10002f54	stdio_init_all	bool stdio_init_all(void)
0x100032a0	stdio_uart_init	void stdio_uart_init(void)
0x10002f2c	stdio_set_driver_enabled	void stdio_set_driver_enabled(stdio_driver_t*, bool)
0x10002d30	stdio_out_chars_crlf	void stdio_out_chars_crlf(stdio_driver_t*, const char*, int)
0x10002e40	stdio_put_string	int stdio_put_string(const char*, int, bool, bool)
0x100030e4	__wrap_printf	int __wrap_printf(const char*, ...)
0x10003020	__wrap_vprintf	int __wrap_vprintf(const char*, va_list)
0x10000248	gpio_set_function	void gpio_set_function(uint, gpio_function_t)
0x10000e10	uart_init	uint uart_init(uart_inst_t*, uint)
0x10000da0	time_us_64	uint64_t time_us_64(void)
0x100033e0	strlen	size_t strlen(const char*)

A void return type may not stick — here is the fix. Binary Ninja treats void as low-confidence, and its analysis can override it with an inferred type — most often int32_t on this 32-bit target. It is most visible on _reset_handler (a hand-written assembly entry that never returns normally), but it can happen to any function whose return type Binary Ninja thinks it can infer.

Setting the full signature with Y reproduces the unwanted int32_t, and fn.return_type = ... fails too. What works is the return-value setter:

from binaryninja import ReturnValue, Type
fn = bv.get_function_at(0x1000015c)
if fn is not None:
    fn.return_value = ReturnValue(Type.void())

That holds _reset_handler at void even after reanalysis (verified live). Setting the signature and the return type both failing while return_value succeeds looks like a bug or inconsistency in this build (BN 6.0.10601). If it still will not stick, leave it — it does not affect the rest of the lesson.

__wrap_printf is the real symbol. printf in our source compiles to the SDK's __wrap_printf (which forwards to __wrap_vprintf). Rename it printf if you prefer the lesson's shorthand, but __wrap_printf is what the ELF says.

stdio_init_all returns bool, not void — _Bool stdio_init_all(void) in the ELF. The main source ignores the return value, so the decompiler still reads fine.

Shortcut — resolves name and type for every function. Instead of doing N + Y by hand, paste this into Binary Ninja's Python console (Plugins -> Python Console). It sets each function's name and signature programmatically:

from binaryninja import Symbol, SymbolType
# The raw .bin has no headers, so these SDK types don't exist. set_user_type()
# re-parses each signature as C, so an undefined name raises
# "SyntaxError: unknown type name '...'". Define them first.
sdk = bv.parse_types_from_string("""
typedef unsigned int uint;
typedef char* va_list;
struct stdio_driver;
typedef struct stdio_driver stdio_driver_t;
struct uart_inst;
typedef struct uart_inst uart_inst_t;
enum gpio_function {
    GPIO_FUNC_XIP = 0, GPIO_FUNC_SPI = 1, GPIO_FUNC_UART = 2, GPIO_FUNC_I2C = 3,
    GPIO_FUNC_PWM = 4, GPIO_FUNC_SIO = 5, GPIO_FUNC_PIO0 = 6, GPIO_FUNC_PIO1 = 7,
    GPIO_FUNC_GPCK = 8, GPIO_FUNC_USB = 9, GPIO_FUNC_NULL = 0x1f,
};
typedef enum gpio_function gpio_function_t;
""")
for name, ty in sdk.types.items():
    bv.define_user_type(name, ty)

# address: (name, signature);  None means "leave the type alone"
funcs = {
    0x1000015c: ("_reset_handler",            "void _reset_handler(void)"),
    0x10000186: ("platform_entry",            "void platform_entry(void)"),
    0x1000019a: ("data_cpy",                  "void data_cpy(void*, void*, void*)"),
    0x100001e4: ("_init",                     "void _init(void)"),
    0x10000210: ("frame_dummy",               "void frame_dummy(void)"),
    0x10000234: ("main",                      "int main(void)"),
    0x10002cfc: ("exit",                      "void exit(int)"),
    0x10002d04: ("runtime_init",              "void runtime_init(void)"),
    0x10002f54: ("stdio_init_all",            "bool stdio_init_all(void)"),
    0x100032a0: ("stdio_uart_init",           "void stdio_uart_init(void)"),
    0x10002f2c: ("stdio_set_driver_enabled",  "void stdio_set_driver_enabled(stdio_driver_t*, bool)"),
    0x10002d30: ("stdio_out_chars_crlf",      "void stdio_out_chars_crlf(stdio_driver_t*, const char*, int)"),
    0x10002e40: ("stdio_put_string",          "int stdio_put_string(const char*, int, bool, bool)"),
    0x100030e4: ("__wrap_printf",             "int __wrap_printf(const char*, ...)"),
    0x10003020: ("__wrap_vprintf",            "int __wrap_vprintf(const char*, va_list)"),
    0x10000248: ("gpio_set_function",         "void gpio_set_function(uint, gpio_function_t)"),
    0x10000e10: ("uart_init",                 "uint uart_init(uart_inst_t*, uint)"),
    0x10000da0: ("time_us_64",                "uint64_t time_us_64(void)"),
    0x100033e0: ("strlen",                    "size_t strlen(const char*)"),
}
for addr, (name, sig) in funcs.items():
    bv.define_user_symbol(Symbol(SymbolType.FunctionSymbol, addr, name))
    if sig:
        f = bv.get_function_at(addr)
        if f is not None:
            f.set_user_type(sig)

SDK type names (stdio_driver_t, gpio_function_t, uart_inst_t, plus uint and va_list) are not in the raw .bin. set_user_type re-parses each signature as C, so an undefined name raises SyntaxError: unknown type name '...' and stops the loop — it is not harmless. The sdk block above defines them first (an opaque struct/enum/typedef is enough to parse). If you add a function that uses another SDK type, add a definition for it to that block too.

Step 17: Read main in the decompiler

Open the Decompiler view on main. It reads:

int32_t main(void)
{
    stdio_init_all();
    do
    {
        printf("age: %d\r\n", 0x2b);
    } while (true);
}

The 0x2b is the value we edited live. Now make it permanent.

Step 18: Patch 0x2b to 0x46 in the GUI

Go to 0x1000023a:

1000023a: 212b   movs  r1, #43 ; 0x2b

The halfword is 0x212b, stored little-endian as 2b 21. The immediate is the low byte, so the byte at the instruction's own address is 0x2b. Change it to 0x46 (70).

Option A — Hex view:

1. Switch to the Hex view (View -> Hex).
2. Toggle the lock off so editing is enabled.
3. Go to 0x1000023a and change the byte 2B to 46.
4. Return to the linear view, right-click the function -> Reanalyze.

Option B — Python console:

bv.write(0x1000023a, b"\x46")
print(hex(bv.read(0x1000023a, 1)[0]))  # -> 0x46

After reanalysis the instruction reads movs r1, #70.

Step 18b: Patch the string age: to foo: in the GUI

The format string "age: %d\r\n" starts at 0x100034a0. Its first three bytes are 61 67 65 (age). Change them to 66 6f 6f (foo), leaving the : %d\r\n tail untouched, so the line prints foo: 70.

Option A — Hex view:

1. Switch to the Hex view (View -> Hex).
2. Go to 0x100034a0 and change the three bytes 61 67 65 to 66 6f 6f.
3. Return to the linear view and reanalyze.

Option B — Python console:

bv.write(0x100034a0, b"foo")
print(bv.read(0x100034a0, 10))  # -> b'foo: %d\r\n\x00'

Keep the replacement exactly three bytes. If you use a shorter string you must pad it, or %d shifts and printf reads the wrong argument. A longer string would overwrite the : %d tail.

Step 19: Export the patched .bin

import os
seg = next(s for s in bv.segments if s.data_length)  # the loadable image segment
data = bv.read(seg.start, seg.data_length)  # base + size come from the view itself
out = os.path.join(os.path.join(root, "0x0005_intro-to-variables", "build"), "0x0005_intro-to-variables-h.bin")
open(out, "wb").write(data)
print(len(data), out)  # -> 15292 /.../build/0x0005_intro-to-variables-h.bin

Where the two numbers come from — nothing is hardcoded:

• seg.start is the image base Binary Ninja loaded the .bin at (0x10000000), the same value you pass to uf2conv --base.
• seg.data_length is the segment's size in the file (0x3bbc = 15292). Exactly one segment carries data (the image); every peripheral and synthetic segment has data_length == 0, so next(...) picks the image.
• Reading seg.start for seg.data_length bytes therefore grabs exactly the image.

Two gotchas this avoids:

• No relative path. Binary Ninja's Python console runs with a read-only working directory (inside the app bundle), so open("0x0005_intro-to-variables-h.bin", "wb") fails with OSError: [Errno 30] Read-only file system. root (from ~/.embedded-hacking-repo, Step 3) is the repo, so the file is written into the project's build/ — no machine-specific path and no database needed.
• Read the image, not the whole view. bv.read(bv.start, bv.length) spans the entire mapped range (0x10000000..0xe008000c), which is not the image. The segment's data_length is the image size.

A different size means you exported a partial view.

Step 20: Convert to UF2

Run from the project directory:

macOS Apple Silicon / Linux x64:

python3 ../uf2conv.py 0x0005_intro-to-variables-h.bin \
  --base 0x10000000 --family 0xe48bff59 --output hacked.uf2

Windows x64:

python ..\uf2conv.py 0x0005_intro-to-variables-h.bin ^
  --base 0x10000000 --family 0xe48bff59 --output hacked.uf2

Or convert from the Binary Ninja console — it is a normal Python interpreter, so you never have to leave the app. chdir to a writable directory first (the default one is read-only), then run the script:

import os, sys, runpy
os.chdir(os.path.join(root, "0x0005_intro-to-variables", "build"))   # the project build dir (writable)
sys.argv = ["uf2conv.py", "0x0005_intro-to-variables-h.bin",
            "--base", "0x10000000", "--family", "0xe48bff59", "--output", "hacked.uf2"]
runpy.run_path("../../uf2conv.py", run_name="__main__")   # path to your uf2conv.py

This writes hacked.uf2 next to the .bin, ready to drag onto the Pico.

Step 21: Flash and verify age: 70

Hold BOOTSEL, plug in the Pico 2, and drag hacked.uf2 onto the RP2350 drive. Open the serial monitor:

age: 70
age: 70
age: 70
...

43 became 70, permanently, with one byte changed and no source code.

Faster: flash over the Debug Probe (no BOOTSEL). The repo's flash.sh writes the raw .bin straight into XIP flash over SWD (program <bin> 0x10000000 verify reset exit), so you never touch BOOTSEL or a UF2. Run it from a terminal (./flash.sh <bin>), or from the Binary Ninja console without freezing it — use subprocess.Popen, which returns immediately, and send OpenOCD's output to a log file. (subprocess.run blocks the console until the flash finishes; do not use it here.)

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()
bin_path = os.path.join(os.path.join(root, "0x0005_intro-to-variables", "build"), "0x0005_intro-to-variables-h.bin")
log = os.path.join(os.path.join(root, "0x0005_intro-to-variables", "build"), "flash.log")
subprocess.run(["pkill", "-TERM", "-f", "openocd"])  # free the probe first
p = subprocess.Popen([os.path.join(root, "flash.sh"), bin_path],
                     stdout=open(log, "w"), stderr=subprocess.STDOUT, start_new_session=True)
print("flashing in the background; log:", log)

The pkill frees the probe first; on Windows use subprocess.run(["taskkill", "/F", "/IM", "openocd.exe"]).

The console is free the moment this returns. Check it with print(p.poll()) (None = still running, 0 = done) or read flash.log — success ends with ** Verified OK **. (Verified: Popen returns in ~1 ms; the flash itself takes ~2 s.)

The same non-blocking form without the script:

import os, subprocess
ocd = os.path.expanduser("~/.pico-sdk/openocd/0.12.0+dev")
bin_path = os.path.join(os.path.join(root, "0x0005_intro-to-variables", "build"), "0x0005_intro-to-variables-h.bin")
log = os.path.join(os.path.join(root, "0x0005_intro-to-variables", "build"), "flash.log")
subprocess.run(["pkill", "-TERM", "-f", "openocd"])  # free the probe first
p = subprocess.Popen([f"{ocd}/openocd", "-s", f"{ocd}/scripts",
    "-f", "interface/cmsis-dap.cfg", "-f", "target/rp2350.cfg",
    "-c", "adapter speed 5000",
    "-c", f"program {bin_path} 0x10000000 verify reset exit"],
    stdout=open(log, "w"), stderr=subprocess.STDOUT, start_new_session=True)
print("flashing in the background; log:", log)

The Debug Probe is single-owner. If Binary Ninja is still attached (the debug-server.sh OpenOCD is running), the flash cannot grab the probe. Detach in Binary Ninja and stop that OpenOCD first:

# macOS / Linux
pkill -TERM -f openocd

# Windows
Get-Process openocd -ErrorAction SilentlyContinue | Stop-Process

Success looks like Programming Finished -> Verified OK -> Resetting Target. On Windows use flash.ps1 (.\flash.ps1 -Bin <path>) the same way.

---

Part 5: Dynamic — Break at main and Hack Live (Project 2)

Step 22: Reflash Project 2 and reload Binary Ninja

Part 4 left the Pico running the patched Project 1 image. Put the original Project 2 back and start a fresh session.

1. Stop any running debug server so the flash script can use the probe:

   # macOS / Linux
   pkill -TERM -f openocd
   

   # Windows
   Get-Process openocd -ErrorAction SilentlyContinue | Stop-Process
   

2. Flash the original Project 2 image:

   # macOS / Linux
   ./flash.sh 0x0008_uninitialized-variables/build/0x0008_uninitialized-variables.bin
   

   # Windows
   .\flash.ps1 -Bin 0x0008_uninitialized-variables\build\0x0008_uninitialized-variables.bin
   

   Or do steps 1–2 from the Binary Ninja console (the active view is still Project 1, so take the repo root from it and point at the Project 2 .bin):

   macOS / Linux:

   import os, subprocess
   root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()  # set once (Step 3)
   bin_path = os.path.join(root, "0x0008_uninitialized-variables", "build", "0x0008_uninitialized-variables.bin")
   log = os.path.join(os.path.dirname(bin_path), "flash.log")
   subprocess.run(["pkill", "-TERM", "-f", "openocd"])  # free the probe first
   subprocess.Popen([os.path.join(root, "flash.sh"), bin_path],
                    stdout=open(log, "w"), stderr=subprocess.STDOUT, start_new_session=True)
   print("flashing Project 2 in the background; log:", log)
   

   Windows:

   import os, subprocess
   root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()  # set once (Step 3)
   bin_path = os.path.join(root, "0x0008_uninitialized-variables", "build", "0x0008_uninitialized-variables.bin")
   log = os.path.join(os.path.dirname(bin_path), "flash.log")
   subprocess.run(["taskkill", "/F", "/IM", "openocd.exe"])  # free the probe first
   subprocess.Popen(["powershell", "-ExecutionPolicy", "Bypass", "-File",
                     os.path.join(root, "flash.ps1"), "-Bin", bin_path],
                    stdout=open(log, "w"), stderr=subprocess.STDOUT)
   print("flashing Project 2 in the background; log:", log)
   

3. Start the debug server again (Step 10) and wait for Listening on port 3333.

4. Load Project 2 and save its database — see Step 22b.

5. Connect Binary Ninja again (Step 11): adapter GDB MI, IP 127.0.0.1, port 3333.

Confirm the Pico prints age: 0 and blinks the red LED.

Step 22b: Load Project 2 into Binary Ninja and save the database

Exactly like Steps 7–8, but for Project 2. Use File -> Open with Options... (not plain File -> Open), select 0x0008_uninitialized-variables/build/0x0008_uninitialized-variables.bin, and set:

• Architecture: thumb2
• Platform: thumb2
• Base Address: 0x10000000

Click Open. Then press G, type 0x10000000, and confirm the first two words:

0x10000000   0x20082000   initial stack pointer
0x10000004   0x1000015d   reset vector (bit 0 = Thumb)

If you see data at 0x00000000, close the tab and redo it with Open with Options.

Save it with File -> Save As... as 0x0008_uninitialized-variables.bndb (next to the .bin). From now on open the .bndb, not the .bin; save with Cmd+S / Ctrl+S after every rename or patch.

Console equivalent:

load("0x0008_uninitialized-variables/build/0x0008_uninitialized-variables.bin",
     options={"loader.imageBase": 0x10000000, "loader.platform": "thumb2"})

Then resolve the functions for Project 2 the same way as Project 1 — Step 26.

Step 23: Break at main

main is at 0x10000234 in this project too. The GUI sets breakpoints fine (Step 13); the only caution is not to drive reset run from the port while Binary Ninja is attached (it desyncs Binary Ninja's view). Use BP_ADDR, which arms main before Binary Ninja connects:

1. Stop the server (Ctrl-C), then start it parked at main:

   # macOS / Linux
   BP_ADDR=0x10000234 ./debug-server.sh
   

   # Windows
   $env:BP_ADDR="0x10000234"; .\debug-server.ps1
   

   Or restart it from the Binary Ninja console — kill any running server, then start it parked at main:

   macOS / Linux:

   import os, subprocess
   root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()
   log = os.path.join(root, "openocd.log")
   subprocess.run(["pkill", "-TERM", "-f", "openocd"])  # kill any running server first
   subprocess.Popen([os.path.join(root, "debug-server.sh")], cwd=root,
                    env=dict(os.environ, BP_ADDR="0x10000234"),
                    stdout=open(log, "w"), stderr=subprocess.STDOUT, start_new_session=True)
   print("OpenOCD restarted parked at main; log:", log)
   

   Windows:

   import os, subprocess
   root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()
   log = os.path.join(root, "openocd.log")
   subprocess.run(["taskkill", "/F", "/IM", "openocd.exe"])  # kill any running server first
   subprocess.Popen(["powershell", "-ExecutionPolicy", "Bypass", "-File",
                     os.path.join(root, "debug-server.ps1")], cwd=root,
                    env=dict(os.environ, BP_ADDR="0x10000234"),
                    stdout=open(log, "w"), stderr=subprocess.STDOUT)
   print("OpenOCD restarted parked at main; log:", log)
   

2. Connect Binary Ninja (Step 11): adapter GDB MI, IP 127.0.0.1, port 3333.

The target is already halted at main when Binary Ninja connects, and the sidebar reads Stopped at 0x10000234.

If you instead want to reach main on an already-connected session, you must Detach, send reset run from the port, then reconnect. Arming main and resetting while attached leaves the sidebar showing a stale address.

main sets up GPIO 16 and then loops: print age, turn the LED on, sleep, turn it off, sleep. The whole loop is one function because blink_and_print was inlined:

10000234 <main>:
10000234: b538         push  {r3, r4, r5, lr}
10000236: f002 ff49    bl    0x100030cc        ; stdio_init_all
1000023a: 2010         movs  r0, #16           ; LED_PIN
1000023c: f000 f83a    bl    0x100002b4        ; gpio_init
10000240: f04f 0501    mov.w r5, #1
10000244: 2310         movs  r3, #16           ; LED_PIN
10000246: ec45 3044    mcrr  0, 4, r3, r5, cr4 ; gpio_set_dir(16, OUT)
1000024a: 2100         movs  r1, #0            ; age
1000024c: 4809         ldr   r0, [pc, #36]     ; @ 0x10000274 -> "age: %d\r\n"
1000024e: f003 f805    bl    0x1000325c        ; __wrap_printf
10000252: 2410         movs  r4, #16           ; LED_PIN
10000254: ec45 4040    mcrr  0, 4, r4, r5, cr0 ; gpio_put(16, 1)
10000258: f44f 70fa    mov.w r0, #500
1000025c: f000 fd58    bl    0x10000d10        ; sleep_ms
10000260: f04f 0300    mov.w r3, #0
10000264: ec43 4040    mcrr  0, 4, r4, r3, cr0 ; gpio_put(16, 0)
10000268: f44f 70fa    mov.w r0, #500
1000026c: f000 fd50    bl    0x10000d10        ; sleep_ms
10000270: e7eb         b.n   0x1000024a
10000272: bf00         nop
10000274: 10003618     .word 0x10003618

Look at the Registers widget at 0x1000024e: r1 is 0, which is why the Pico prints age: 0.

Step 24: Inspect the GPIO registers live

The GPIO hardware is memory-mapped. Go to each address and watch it change as you step:

Address	Block	Role
0x40028000	IO_BANK0	pin function select and status
0x40038000	PADS_BANK0	pad configuration
0xd0000000	SIO	single-cycle GPIO block driven by mcrr

Step Over through 0x10000254 (mcrr 0, 4, r4, r5, cr0) and watch the SIO output register change: this is gpio_put(16, 1) turning the red LED on at the hardware level.

Step 25: HACK IT LIVE — change the printed value

1. Press G, go to 0x1000024e (the bl __wrap_printf).

2. Set a hardware execute breakpoint at 0x1000024e in the GUI (Debugger -> Add Hardware Breakpoint...; not F2). Note 0x1000024e — Project 2's loop sits at a different address than Project 1's.

3. Click Resume in Binary Ninja. The target is already looping, so the breakpoint fires on the next pass. Binary Ninja stops with r1 = 0.

4. Set r1 to 0x42 (66):

   dbg.set_reg_value("r1", 0x42)
   

   (Or right-click r1 in the Registers widget, press E, type 42, and press Enter.)

5. Move the breakpoint past the call. 0x10000252 is the instruction right after the bl __wrap_printf. Remove the breakpoint at 0x1000024e and set a hardware breakpoint at 0x10000252, then click Resume. The core runs printf with r1 = 0x42 and stops at 0x10000252. (Not Step Over — it steps into the call on this symbol-less .bin, and a breakpoint left on the current PC re-traps the step; Step 13 explains both.)

6. Look at your serial monitor and the Target tab:

   age: 66
   

Press Resume and the next iteration prints age: 0 again, because the loop reloads movs r1, #0 each pass. The live hack is temporary; the static patch makes it permanent.

Step 25b: HACK THE STRING LIVE — change age: to foo:

Same idea as Project 1, different addresses. Here the format string is at 0x10003618 and the printf call is at 0x1000024e.

1. Hit the breakpoint at 0x1000024e as in Step 25. At the stop, r0 = 0x10003618 and r1 = 0.
2. Write the replacement string to free RAM at 0x20080000 from the Python console (dbg.write_memory — no command port needed):

   dbg.write_memory(0x20080000, b"foo: %d\r\n\x00")
   

   Bytes 66 6f 6f 3a 20 25 64 0d 0a 00 = "foo: %d\r\n\0".
3. Point r0 at that string:

   dbg.set_reg_value("r0", 0x20080000)
   

   (Or right-click r0 in the Registers widget, press E, type 0x20080000, and press Enter.)
4. Move the breakpoint past the call in the GUI (remove it at 0x1000024e, set one at 0x10000252) and click Resume. This iteration prints:

   foo: 0
   

   then stops at 0x10000252. One iteration only — the loop reloads r0 each pass. The permanent version is the static patch in Step 28b.

Step 25c: Kill the debugger and OpenOCD

Same as Step 15b: click the X (Kill) in the Debugger sidebar (or Debugger -> Kill), then stop OpenOCD from the Binary Ninja console:

macOS / Linux:

import subprocess
subprocess.run(["pkill", "-TERM", "-f", "openocd"])  # stop the debug server, free the probe

Windows:

import subprocess
subprocess.run(["taskkill", "/F", "/IM", "openocd.exe"])  # stop the debug server, free the probe

---

Part 6: Static — Resolve the Functions and Patch (Project 2)

Step 26: Resolve the functions in the Binary Ninja GUI

Same two keys as Step 16 — G to the address, then Y (Change Type) to set the prototype — using the Project 2 ELF symbol map from Step 4.

The mechanics are identical to Step 16, so here are the worked examples for the functions that are specific to this project.

main

1. G -> 0x10000234.
2. Y -> int main(void) (Binary Ninja shows int32_t main(void) — the same 32-bit int).

gpio_init

1. G -> 0x100002b4.
2. Y -> void gpio_init(uint gpio).

sleep_ms

1. G -> 0x10000d10.
2. Y -> void sleep_ms(uint32_t ms).

stdio_init_all and __wrap_printf

Same as Project 1, different addresses: stdio_init_all at 0x100030cc (bool stdio_init_all(void)), and __wrap_printf at 0x1000325c (int __wrap_printf(const char *fmt, ...)).

Then work down the table the same way.

Same idea as Project 1: our code plus what it calls, not the whole SDK. The call chain here is one function longer because main also drives the GPIO and sleeps:

main
├── stdio_init_all
│   ├── stdio_uart_init ── gpio_set_function, uart_init
│   ├── stdio_set_driver_enabled
│   ├── stdio_out_chars_crlf
│   ├── stdio_put_string ── strlen
│   └── time_us_64
├── gpio_init
├── __wrap_printf ── __wrap_vprintf
└── sleep_ms

Two things in this project have no symbol of their own, because the compiler inlined them into main:

• blink_and_print — the static helper in our own source is inlined, so there is no blink_and_print address to rename. You see its body directly inside main.
• gpio_set_dir and gpio_put — these are static inline in the SDK headers, so they compile to the mcrr/SIO writes you see in main rather than to calls.

Project 2 — resolve every function in that chain:

Address	Rename to (N)	Signature (Y)
0x1000015c	_reset_handler	void _reset_handler(void)
0x10000186	platform_entry	void platform_entry(void)
0x1000019a	data_cpy	void data_cpy(void*, void*, void*)
0x100001e4	_init	void _init(void)
0x10000210	frame_dummy	void frame_dummy(void)
0x10000234	main	int main(void)
0x100002b4	gpio_init	void gpio_init(uint)
0x10000278	gpio_set_function	void gpio_set_function(uint, gpio_function_t)
0x10000d10	sleep_ms	void sleep_ms(uint32_t)
0x10002e74	exit	void exit(int)
0x10002e7c	runtime_init	void runtime_init(void)
0x100030cc	stdio_init_all	bool stdio_init_all(void)
0x10003418	stdio_uart_init	void stdio_uart_init(void)
0x100030a4	stdio_set_driver_enabled	void stdio_set_driver_enabled(stdio_driver_t*, bool)
0x10002ea8	stdio_out_chars_crlf	void stdio_out_chars_crlf(stdio_driver_t*, const char*, int)
0x10002fb8	stdio_put_string	int stdio_put_string(const char*, int, bool, bool)
0x1000325c	__wrap_printf	int __wrap_printf(const char*, ...)
0x10003198	__wrap_vprintf	int __wrap_vprintf(const char*, va_list)
0x10000f88	uart_init	uint uart_init(uart_inst_t*, uint)
0x10000ef4	time_us_64	uint64_t time_us_64(void)
0x10003558	strlen	size_t strlen(const char*)

Python console shortcut (resolves name and type):

from binaryninja import Symbol, SymbolType
# The raw .bin has no headers, so these SDK types don't exist. set_user_type()
# re-parses each signature as C, so an undefined name raises
# "SyntaxError: unknown type name '...'". Define them first.
sdk = bv.parse_types_from_string("""
typedef unsigned int uint;
typedef char* va_list;
struct stdio_driver;
typedef struct stdio_driver stdio_driver_t;
struct uart_inst;
typedef struct uart_inst uart_inst_t;
enum gpio_function {
    GPIO_FUNC_XIP = 0, GPIO_FUNC_SPI = 1, GPIO_FUNC_UART = 2, GPIO_FUNC_I2C = 3,
    GPIO_FUNC_PWM = 4, GPIO_FUNC_SIO = 5, GPIO_FUNC_PIO0 = 6, GPIO_FUNC_PIO1 = 7,
    GPIO_FUNC_GPCK = 8, GPIO_FUNC_USB = 9, GPIO_FUNC_NULL = 0x1f,
};
typedef enum gpio_function gpio_function_t;
""")
for name, ty in sdk.types.items():
    bv.define_user_type(name, ty)

# address: (name, signature);  None means "leave the type alone"
funcs = {
    0x1000015c: ("_reset_handler",            "void _reset_handler(void)"),
    0x10000186: ("platform_entry",            "void platform_entry(void)"),
    0x1000019a: ("data_cpy",                  "void data_cpy(void*, void*, void*)"),
    0x100001e4: ("_init",                     "void _init(void)"),
    0x10000210: ("frame_dummy",               "void frame_dummy(void)"),
    0x10000234: ("main",                      "int main(void)"),
    0x100002b4: ("gpio_init",                 "void gpio_init(uint)"),
    0x10000278: ("gpio_set_function",         "void gpio_set_function(uint, gpio_function_t)"),
    0x10000d10: ("sleep_ms",                  "void sleep_ms(uint32_t)"),
    0x10002e74: ("exit",                      "void exit(int)"),
    0x10002e7c: ("runtime_init",              "void runtime_init(void)"),
    0x100030cc: ("stdio_init_all",            "bool stdio_init_all(void)"),
    0x10003418: ("stdio_uart_init",           "void stdio_uart_init(void)"),
    0x100030a4: ("stdio_set_driver_enabled",  "void stdio_set_driver_enabled(stdio_driver_t*, bool)"),
    0x10002ea8: ("stdio_out_chars_crlf",      "void stdio_out_chars_crlf(stdio_driver_t*, const char*, int)"),
    0x10002fb8: ("stdio_put_string",          "int stdio_put_string(const char*, int, bool, bool)"),
    0x1000325c: ("__wrap_printf",             "int __wrap_printf(const char*, ...)"),
    0x10003198: ("__wrap_vprintf",            "int __wrap_vprintf(const char*, va_list)"),
    0x10000f88: ("uart_init",                 "uint uart_init(uart_inst_t*, uint)"),
    0x10000ef4: ("time_us_64",                "uint64_t time_us_64(void)"),
    0x10003558: ("strlen",                    "size_t strlen(const char*)"),
}
for addr, (name, sig) in funcs.items():
    bv.define_user_symbol(Symbol(SymbolType.FunctionSymbol, addr, name))
    if sig:
        f = bv.get_function_at(addr)
        if f is not None:
            f.set_user_type(sig)

The decompiler now shows main initializing GPIO 16 and looping. We make two changes:

• Move the LED from GPIO 16 to GPIO 17 by patching three 0x10 immediates.
• Change the printed value from 0 to 66 by patching one 0x00 immediate.

Step 27: Patch 1 — move the LED from GPIO 16 to GPIO 17

GPIO 16 is the red LED; GPIO 17 is the green LED. The pin number appears in three instructions. Change the low byte of each from 10 to 11:

Address	Instruction	Bytes before	Bytes after	Role
0x1000023a	movs r0, #16	10 20	11 20	pin passed to gpio_init
0x10000244	movs r3, #16	10 23	11 23	pin used by gpio_set_dir
0x10000252	movs r4, #16	10 24	11 24	pin used by gpio_put in the blink loop

In the Hex view (lock off), change each byte and reanalyze. Or in the Python console:

for addr in (0x1000023a, 0x10000244, 0x10000252):
    bv.write(addr, b"\x11")

All three are required. If you patch only the gpio_set_dir site, pin 17's output driver is enabled but gpio_put still drives pin 16, whose driver was never enabled. Nothing lights up. This is the most common mistake in this lesson.

Step 28: Patch 2 — change the printed value from 0 to 66

main loads age = 0 with movs r1, #0 at 0x1000024a. Change the immediate byte from 00 to 42 (0x42 = 66):

bv.write(0x1000024a, b"\x42")

Verify all four patches:

for addr in (0x1000023a, 0x10000244, 0x10000252, 0x1000024a):
    print(hex(addr), hex(bv.read(addr, 1)[0]))
# -> 0x1000023a 0x11
# -> 0x10000244 0x11
# -> 0x10000252 0x11
# -> 0x1000024a 0x42

Step 28b: Patch the string age: to foo:

The format string starts at 0x10003618; change its first three bytes 61 67 65 (age) to 66 6f 6f (foo):

bv.write(0x10003618, b"foo")
print(bv.read(0x10003618, 10))  # -> b'foo: %d\r\n\x00'

Exactly three bytes, same rule as Project 1: a shorter string must be padded, a longer one overwrites the : %d tail.

Step 29: Export, convert, and flash

import os
seg = next(s for s in bv.segments if s.data_length)  # the loadable image segment
data = bv.read(seg.start, seg.data_length)  # base + size from the view itself
out = os.path.join(os.path.join(root, "0x0008_uninitialized-variables", "build"), "0x0008_uninitialized-variables-h.bin")
open(out, "wb").write(data)
print(len(data), out)  # -> 15668 /.../build/0x0008_uninitialized-variables-h.bin

Same as Project 1: seg.start is the load base and seg.data_length is the image size (here 0x3d34 = 15668) — both read from the view, and no relative path (the console's CWD is read-only).

macOS Apple Silicon / Linux x64:

python3 ../uf2conv.py 0x0008_uninitialized-variables-h.bin \
  --base 0x10000000 --family 0xe48bff59 --output hacked.uf2

Windows x64:

python ..\uf2conv.py 0x0008_uninitialized-variables-h.bin ^
  --base 0x10000000 --family 0xe48bff59 --output hacked.uf2

Or run the conversion from the Binary Ninja console, exactly as in Step 20 (os.chdir to the build dir, then runpy.run_path("../../uf2conv.py", run_name="__main__") with sys.argv set to the arguments above).

Hold BOOTSEL, plug in the Pico 2, drag hacked.uf2 onto the RP2350 drive. Or flash the .bin over the Debug Probe with SWD — no BOOTSEL — from the console, exactly as in Step 21 (stop any running OpenOCD first, and use Popen, not run, so the console is not blocked):

import os, subprocess
root = open(os.path.expanduser("~/.embedded-hacking-repo")).read().strip()
bin_path = os.path.join(os.path.join(root, "0x0008_uninitialized-variables", "build"), "0x0008_uninitialized-variables-h.bin")
log = os.path.join(os.path.join(root, "0x0008_uninitialized-variables", "build"), "flash.log")
subprocess.run(["pkill", "-TERM", "-f", "openocd"])  # free the probe first
p = subprocess.Popen([os.path.join(root, "flash.sh"), bin_path],
                     stdout=open(log, "w"), stderr=subprocess.STDOUT, start_new_session=True)
print("flashing in the background; log:", log)

Step 30: Verify

Open the serial monitor:

age: 66
age: 66
age: 66
...

The green LED on GPIO 17 now blinks instead of the red one.

We changed the printed value and moved the LED, with four bytes and no source code.

---

Cheatsheet

Binary Ninja GUI actions

Action	How
Go to address	G
Rename function/symbol	N
Set type or signature	Y
Add comment	;
Open Hex view	View -> Hex
Enable hex editing	Toggle the lock in the status bar
Reanalyze after a patch	Right-click function -> Reanalyze
Edit a register live	dbg.set_reg_value("r1", 0x46) in the Python console (or right-click the register, press E, type hex, Enter)
Set a breakpoint	Debugger -> Add Hardware Breakpoint... (hardware execute). Do not use F2 — software breakpoints cannot be written to read-only flash.
Move a breakpoint	Remove it and set it at the new address in the GUI (command-port fallback: rbp <old addr> then bp <new addr> 2 hw)
Confirm what is armed	The Breakpoints widget lists it (command-port fallback: mdw 0xE0002000 8, each armed breakpoint shows as <addr | 1>)
Apply the ELF symbol map	Paste the Python snippet from Step 16 / 26 into the Python Console

OpenOCD server and reset

The server runs with gdb_breakpoint_override hard so that flash-writes are never attempted. Breakpoints in this lab are set in the Binary Ninja GUI through the GDB MI adapter (Step 13). The command-port rows below are the fallback if you use the GDB RSP adapter instead.

Action	Command
Connect to the OpenOCD prompt (fallback)	nc 127.0.0.1 4444 (or telnet 127.0.0.1 4444)
Reset and run (command port)	reset run
Check core state (command port)	targets
Set a breakpoint in the GUI	Debugger -> Add Hardware Breakpoint... (hardware execute; F2 software breakpoints do not work on flash)
(fallback) Add a breakpoint without the GUI	bp <addr> 2 hw
Remove one breakpoint	rbp <addr> — address only, no length, no hw
Remove every breakpoint	rbp all
Start the server parked at main	macOS/Linux: BP_ADDR=0x10000234 ./debug-server.sh — Windows: $env:BP_ADDR="0x10000234"; .\debug-server.ps1 (one-shot)
Start the server parked in the loop	macOS/Linux: BP_ADDR=0x1000023e ./debug-server.sh — Windows: $env:BP_ADDR="0x1000023e"; .\debug-server.ps1 (0x1000024e for Project 2)
Break on the loop in a running target	set a hardware breakpoint in the GUI at the loop address, then Resume — repeatable
Make Binary Ninja stepping work	rp2350.dap.core0 configure -rtos none (already in the scripts)
Step without re-trapping	move the breakpoint off the current PC first, then Step Into/Step Over
Reset without desyncing Binary Ninja	Detach, reset run on the port, reconnect — never reset run while attached

Every address and byte we changed

Project	Address	Before	After	Effect
0x0005	0x1000023a	2b	46	prints age: 70
0x0008	0x1000023a	10	11	gpio_init configures GPIO 17
0x0008	0x10000244	10	11	gpio_set_dir enables GPIO 17
0x0008	0x10000252	10	11	gpio_put drives GPIO 17
0x0008	0x1000024a	00	42	prints age: 66
0x0005	0x100034a0	61 67 65	66 6f 6f	string prints foo: instead of age:
0x0008	0x10003618	61 67 65	66 6f 6f	string prints foo: instead of age:

Raw image facts

Item	Value
Build type	Release
Load base address	0x10000000
Project 1 size	15292 bytes
Project 2 size	15668 bytes
Fixed main anchor (both projects)	0x1000018c (reset handler middle blx)
main (both projects)	0x10000234
printf call, Project 1	0x1000023e
printf call, Project 2	0x1000024e
RP2350 UF2 family ID	0xe48bff59

---

Troubleshooting

Binary Ninja hangs or crashes when you connect (macOS 27)

Three different causes have been seen on this setup; check them in this order.

• A breakpoint set before connecting. With the GDB MI adapter, if the binary view already has a breakpoint, the session hangs. Start parked with BP_ADDR, connect, then add breakpoints (see the next entry).
• The wrong GDB executable. Point Full GDB Executable Path at the 14.2.rel1 toolchain (Step 11). The 13.3.rel1 build (what /opt/homebrew/bin/arm-none-eabi-gdb symlinks to) did not connect in testing.
• The LLDB adapter. A crash report with libdebuggercore.dylib -> std::terminate() -> abort() and liblldb in the stack is the LLDB adapter, not GDB MI. Avoid LLDB on this setup.

Use GDB MI, with the 14.2.rel1 path above. If it still fails, fall back to plain arm-none-eabi-gdb against the same server — the addresses and register values are identical to the GUI steps.

If Binary Ninja hangs, force-quit it; the connect dialog has no working Cancel. The static steps (resolve, patch, export, flash) never touch the debugger and always work.

The GUI refuses to set a breakpoint (GDB RSP adapter only)

If you are on the GDB RSP adapter, the GUI cannot set breakpoints on this target. That adapter is Binary Ninja's own minimal RSP client and sends a 1-byte breakpoint (Z0,<addr>,1); the Cortex-M33 comparators need 2 bytes, so OpenOCD answers only breakpoints of two bytes length supported. It affects every address, both Toggle Breakpoint and Add Hardware Breakpoint, and the dialog's Size field is disabled. gdb_breakpoint_override makes no difference.

Fix: use the GDB MI adapter (Step 11). It drives real GDB, which sends the correct length, so GUI breakpoints just work. If you must stay on GDB RSP, arm breakpoints from the command port after connecting (bp <addr> 2 hw) — but the lab uses GDB MI and does not need that.

GDB MI hangs when you connect (a breakpoint already existed)

With the GDB MI adapter, if Binary Ninja already has a breakpoint set when you connect, the session hangs. This is a Binary Ninja bug. The working order is:

1. Start the server parked, e.g. BP_ADDR=0x10000234 ./debug-server.sh (Windows: $env:BP_ADDR="0x10000234"; .\debug-server.ps1).
2. Connect with the GDB MI adapter.
3. Only then set hardware breakpoints in the UI.

Never have a breakpoint in the binary view before the GDB MI connection. If it hangs, quit Binary Ninja, restart the server with BP_ADDR, and connect again before adding any breakpoints.

Step Into / Step Over does nothing (PC never moves)

Two causes have been seen on this target.

1. A breakpoint on the current PC re-traps the step. OpenOCD's step-over-breakpoint logic fails with Duplicate Breakpoint address and the PC stays put. Fix: move the breakpoint off the current PC (in the GUI), then step.
2. The hwthread RTOS (GDB RSP adapter only). With the GDB RSP adapter, OpenOCD can log fake step thread 0 and reply without stepping, because the RP2350 config's -rtos hwthread makes the current thread id 1 while Binary Ninja sends thread id 0. Fix: rp2350.dap.core0 configure -rtos none (the launcher scripts already pass this). GDB MI does not hit this.

To tell them apart, turn on OpenOCD logging (log_output /tmp/ocd.log, then debug_level 3 on the command port) and look for fake step versus Duplicate Breakpoint.

zsh: bad CPU type in executable: cmake

An Intel x86_64 tool is on your PATH on Apple Silicon. Run Step 2: export PATH="/opt/homebrew/bin:$PATH", then hash -r. Add it to ~/.zshrc to make it permanent.

My addresses do not match this guide

You probably built Debug. This lesson is a Release build. Re-run Step 3 with -DCMAKE_BUILD_TYPE=Release. A Debug build moves the SDK functions and keeps blink_and_print separate, so Project 2's main is not at 0x10000234.

A breakpoint never fires

First, confirm you actually set one, and that it is a hardware breakpoint. With the GDB MI adapter, Debugger -> Add Hardware Breakpoint... (hardware execute) should land in the Breakpoints widget. If nothing lands, or the core keeps running, you probably used F2 (Toggle Breakpoint) — that is a software breakpoint and cannot be written to read-only flash, so it never installs. Also check you are on GDB MI, not GDB RSP (the GDB RSP adapter cannot set breakpoints on this target at all).

Then check the order and the state:

• Arm it only after Binary Ninja is connected. OpenOCD flushes every breakpoint when a client attaches (breakpoint_remove_all_internal -> Delete all breakpoints), so anything armed earlier is gone. This also applies to BP_ADDR on the startup command line, and to hbreak followed by detach in GDB.
• Verify it is armed: mdw 0xE0002000 8. You should see your address with the low bit set (0x10000234 -> 0x10000235). All zeros means nothing is armed — re-read this first, because it distinguishes "not armed" from "armed but never reached".
• Is the core running? poll on the command port should not report a halt. If it is stopped, click Resume.
• Does the address get reached again? main runs once per reset, so use BP_ADDR at startup (Step 10) rather than reset run while attached. Loop addresses such as 0x1000023e fire on the next pass with no reset — arm them and click Resume in Binary Ninja.
• With GDB MI the stop is reported as Breakpoint and appears in the Breakpoints widget, because GDB really did set it. (On the old GDB RSP workaround the stop showed as SingleStep with an empty widget, because the breakpoint was armed behind Binary Ninja's back.)

I edit r1 (or another register) and it reverts

main reloads the value at the top of every loop iteration — movs r1, #43 at 0x1000023a runs right before the printf at 0x1000023e. So r1 is only 0x46 for the instant between your edit and the next pass; then it is 0x2b again. The edit sticks only if the core is genuinely stopped at the breakpoint and stays stopped.

If it keeps reverting, the core is running, which almost always means the breakpoint is not installed — usually because it is a software breakpoint (F2) that cannot be written to read-only flash. Use Debugger -> Add Hardware Breakpoint... (hardware execute). Confirm with mdw 0xE0002000 4 on the command port: a hardware breakpoint shows as 0x1000023f; all zeros means nothing is armed.

The Registers widget is a snapshot, not a live view. Binary Ninja reads the registers at each stop and shows that snapshot; it does not poll the target, and there is no "refresh registers" command (only "Force Update Memory Cache", which is for memory). So a value changed outside Binary Ninja will not appear until the next stop.

The serial capture is garbage on macOS

Reading /dev/cu.usbmodem* with a bare read() returns garbage. Set raw termios at 115200 first: clear canonical/echo flags, set CLOCAL|CREAD, and B115200 on input and output. screen /dev/cu.usbmodem* 115200 does all of this for you; a script must call tcsetattr itself. Once set, the capture reads clean age: 43 lines.

It worked for a second, then stopped (Binary Ninja's view desyncs)

This is the most common failure, and it has one main cause: driving the core from the OpenOCD command port while Binary Ninja is connected.

• If you send reset run from the port while attached, the core resets, runs, and halts at your breakpoint — but Binary Ninja never receives the stop event. Its sidebar keeps showing the previous location, so Step and Resume act on a stale PC and appear to do nothing. Verified: target at 0x1000023e while the sidebar still read Stopped at 0x10003020.
• If the OpenOCD process dies (or you restart it) while attached, Binary Ninja keeps believing it is connected: the sidebar stays, but the menu shows Pause enabled and Resume/Step disabled because Binary Ninja last saw the target running.

Recovery: Detach, then reconnect. If Detach does nothing (the connection is already dead), restart Binary Ninja — its menu still shows a session that no longer exists.

Prevention:

• Stop at main with BP_ADDR on a fresh server start, not with reset run while attached.
• For loop addresses, set the breakpoint in the GUI and click Resume. Let Binary Ninja be the thing that starts the core.
• If you must reset, Detach first, reset run, then reconnect.
• Never leave a breakpoint on the PC you are about to step or resume from (see the stepping section above).

If the stop is at 0x1000320c rather than your breakpoint, you stopped inside stdio_uart_out_flush, not at main. See the next section.

The target "blows past" main and stops at 0x1000320c instead

0x1000320c is inside stdio_uart_out_flush:

1000320c: 6993   ldr  r3, [r2, #24]
1000320e: 071b   lsls r3, r3, #28
10003210: d4fc   bmi.n 0x1000320c

That is the UART transmit-FIFO drain loop inside printf, so the core is running main's loop and simply spends nearly all its time there. The breakpoint at main did not fire because main's entry (0x10000234) runs exactly once per reset. If you arm the breakpoint after the reset, or set it while the target is already running and just resume, the core is already past 0x10000234 and will never re-execute it. Either arm the breakpoint before resetting, or break inside the loop at 0x1000023e, which fires every iteration.

0x1000320c is not a function. It is one instruction inside stdio_uart_out_flush, which starts at 0x10003208:

10003208 <stdio_uart_out_flush>:
10003208: 4b02   ldr  r3, [pc, #8]  ; @ 0x10003214
1000320a: 681a   ldr  r2, [r3]
1000320c: 6993   ldr  r3, [r2, #24] ; the core sits here while the UART drains
1000320e: 071b   lsls r3, r3, #28
10003210: d4fc   bmi.n 0x1000320c
10003212: 4770   bx lr
10003214: 20000850 .word 0x20000850

If Binary Ninja has created a function at 0x1000320c (for example because the debugger stopped at that PC), the decompiler shows garbage: registers named entry_r4/entry_r5, and stores to invented constants like 0x3a and 0xfffffff6. Delete that bogus function (right-click it -> Delete Function, or put the cursor on it and press U to undefine) and reanalyze. The real function is stdio_uart_out_flush at 0x10003208.

The console floods with Failed to read memory at 0xf0000000

Core1 is exposed. The scripts must run with USE_CORE=0. Stop the server, confirm only core0 is reported, restart, then restart Binary Ninja.

Connect to Remote Process is greyed out and Pause does nothing

Binary Ninja is in a stale session, usually because the debug server restarted while attached. Quit and reopen Binary Ninja (or the .bndb) and connect again.

The decompiler still shows the old value after patching

Right-click the function and choose Reanalyze.

Project 2's LED does not light at all after patching

You patched only some of the three GPIO 16 sites. All three of 0x1000023a, 0x10000244, and 0x10000252 must change.

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Fallback: do the dynamic steps with GDB (macOS 27)

If Binary Ninja's debugger crashes on attach on macOS 27 (see Troubleshooting), you can still do the live hack with the ARM GDB from the toolchain, against the same OpenOCD server. The addresses and register values are identical to the GUI steps.

Start the debug server (Step 10), then in a new terminal:

arm-none-eabi-gdb

At the (gdb) prompt:

set architecture armv8-m.main
target extended-remote :3333
hbreak *0x1000023e
continue

Do not run monitor reset run before hbreak. 0x1000023e is inside main's loop, so the breakpoint fires on the next iteration with no reset. If you reset first, the core runs main and you will not catch it.

GDB stops at the printf call. Confirm the value, change it, and let it run:

info registers pc r1  # pc = 0x1000023e, r1 = 0x2b
set $r1 = 0x46
stepi
continue

The serial monitor prints age: 70 for the iteration you changed — the same temporary live hack as editing r1 in the Binary Ninja Registers widget. When you are done, press Ctrl-C, then detach and quit.

If you specifically want to stop at main (0x10000234), remember its entry runs only once per reset, so the breakpoint must be armed before the reset:

monitor reset halt
hbreak *0x10000234
continue

If you instead set it while the target is running and just continue, you will "blow past" main and catch the core inside printf — in this build at 0x1000320c, the stdio_uart_out_flush UART-drain loop.

Project 2 is the same with the other call site and value:

hbreak *0x1000024e
continue
info registers pc r1  # pc = 0x1000024e, r1 = 0
set $r1 = 0x42
stepi

hbreak sets a hardware breakpoint, which is required for read-only flash. It works from plain GDB because GDB sends the 2-byte length the Cortex-M33 comparators need. Binary Ninja's GDB MI adapter goes through the same GDB, so its GUI breakpoints work too; the old GDB RSP adapter was the one that sent a 1-byte length and could not set breakpoints here.

Glossary

Term	Definition
.bss	Section for uninitialized global variables; zeroed by startup code
.data	Section for initialized global variables; copied from flash to SRAM at boot
.elf	Linked image with the symbol table; the ground truth for addresses and names
.rodata	Read-only section for constants and string literals; stays in flash
GPIO	General Purpose Input/Output — controllable pins on the microcontroller
Hardware breakpoint	A breakpoint serviced by the CPU comparators, required for read-only flash
Inlining	The optimizer replacing a function call with the function body; why blink_and_print disappears in Release
Literal pool	A block of 32-bit constants that Thumb-2 code reaches with PC-relative ldr
MMIO	Memory-mapped I/O — hardware registers accessed as memory addresses
SIO	Single-cycle I/O — the fast GPIO block in the RP2350, at 0xd0000000
Thumb bit	Bit 0 of a Cortex-M function pointer; selects Thumb instruction mode
UF2	USB Flashing Format — the file format the Pico 2 bootloader accepts
Vector table	The first words of flash: initial stack pointer and exception vectors

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Remember: the ELF tells you what every address is, and the .bin is what you actually patch. Prove the behavior dynamically, resolve the names from the ELF, then patch the bytes and flash.